[Analogue-commits] r193 - in pkg: R inst

[noreply at r-forge.r-project.org]

Author: gsimpson
Date: 2010-09-29 17:56:24 +0200 (Wed, 29 Sep 2010)
New Revision: 193

Modified:
   pkg/R/tran.R
   pkg/inst/ChangeLog
Log:
improve the replacement of missing values

Modified: pkg/R/tran.R
===================================================================
--- pkg/R/tran.R	2010-09-22 16:23:26 UTC (rev 192)
+++ pkg/R/tran.R	2010-09-29 15:56:24 UTC (rev 193)
@@ -4,6 +4,10 @@
 
 `tran.default` <- function(x, method, a = 1, b = 0, p = 2, base = exp(1),
                    na.rm = FALSE, na.value = 0, ...) {
+    repMissing <- function(x, na.value) {
+        x[is.na(x)] <- na.value
+        return(x)
+    }
     wasDF <- is.data.frame(x)
     dim.nams <- dimnames(x)
     x <- data.matrix(x)
@@ -32,9 +36,7 @@
                     center = scale(x, scale = FALSE, center = TRUE),
                     percent = sweep(x, 1, rowSums(x), "/") * 100,
                     proportion = sweep(x, 1, rowSums(x), "/"),
-                    missing = apply(x, 2,
-                    function(x) {x[is.na(x)] <- na.value
-                                 x}),
+                    missing = repMissing(x, na.value),
                     pcent2prop = x / 100,
                     prop2pcent = x * 100,
                     logRatio = {x <- sweep(x, 2, a, "*")

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2010-09-22 16:23:26 UTC (rev 192)
+++ pkg/inst/ChangeLog	2010-09-29 15:56:24 UTC (rev 193)
@@ -16,6 +16,8 @@
 	species in order to fit the principal curve. 'initCurve'
 	implements several methods for initialising the principal curve.
 
+	* tran: improvements to the underlying code.
+
 Version 0.6-26
 
 	* abernethy: New data set containing the classic Abernethy Forest